FMR1NB

Summary

FMR1NB (FMR1 neighbor, HGNC:26372) is a protein-coding gene on chromosome Xq27.3-q28, encoding FMR1 neighbor protein (Q8N0W7).

Predicted to be located in membrane.

Source: NCBI Gene 158521 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 43 total
• MANE Select transcript: NM_152578

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26372
Approved symbol	FMR1NB
Name	FMR1 neighbor
Location	Xq27.3-q28
Locus type	gene with protein product
Status	Approved
Aliases	FLJ25736, NY-SAR-35, CT37
Ensembl gene	ENSG00000176988
Ensembl biotype	protein_coding
Entrez	158521

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 nonsense_mediated_decay

ENST00000370467, ENST00000489034

RefSeq mRNA: 1 — MANE Select: NM_152578 NM_152578

CCDS: CCDS14683

Canonical transcript exons

ENST00000370467 — 6 exons

Exon	Start	End
ENSE00001256406	148006702	148006842
ENSE00001256413	148003201	148003320
ENSE00001256423	148024865	148025013
ENSE00001452791	147981337	147981679
ENSE00001852824	148026502	148026665
ENSE00003747498	148008618	148008711

Expression profiles

Bgee: expression breadth broad, 39 present calls, max score 95.18.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1407 / max 58.6410, expressed in 29 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
197923	0.1149	26
197924	0.0183	8
197925	0.0075	2

Top tissues by expression

167 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	95.18	gold quality
left testis	UBERON:0004533	94.01	gold quality
testis	UBERON:0000473	91.35	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.12	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.78	gold quality
adult organism	UBERON:0007023	65.63	gold quality
lower lobe of lung	UBERON:0008949	54.80	silver quality
cerebellar vermis	UBERON:0004720	53.28	gold quality
mucosa of transverse colon	UBERON:0004991	47.25	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
right uterine tube	UBERON:0001302	43.32	silver quality
right lobe of liver	UBERON:0001114	42.97	silver quality
thymus	UBERON:0002370	42.81	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
buccal mucosa cell	CL:0002336	42.35	gold quality
sperm	CL:0000019	41.87	gold quality
vastus lateralis	UBERON:0001379	41.41	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
amniotic fluid	UBERON:0000173	40.69	gold quality
placenta	UBERON:0001987	40.61	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality
biceps brachii	UBERON:0001507	40.57	gold quality
upper leg skin	UBERON:0004262	40.57	silver quality
epithelium of nasopharynx	UBERON:0001951	40.45	gold quality
myocardium	UBERON:0002349	40.45	gold quality
gingival epithelium	UBERON:0001949	40.43	gold quality
germinal epithelium of ovary	UBERON:0001304	40.33	gold quality
esophagus squamous epithelium	UBERON:0006920	40.29	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-CURD-11	yes	129.20
E-ANND-3	no	2.45

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

42 targeting FMR1NB, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548J-5P	99.94	71.14	3489
HSA-MIR-548O-5P	99.94	71.24	3488
HSA-MIR-548W	99.94	71.24	3488
HSA-MIR-548Y	99.94	71.28	3514
HSA-MIR-488-3P	99.61	68.79	1731
HSA-MIR-155-5P	99.35	70.16	1509

Literature-anchored findings (GeneRIF, showing 3)

• The analysis of methylation status of the NY-SAR-35 gene promoter in various cancer cell lines showed that its expression was related to methylation of the promoter region. (PMID:21318630)
• NY-SAR35 was predominantly expressed at the cytoplasm. (PMID:26648093)
• used a next generation sequencing (NGS) approach. NY-SAR-35 expression induced growth, proliferation, metastasis, and stemness genes, as indicated by the up-regulations of CXCR4, EpCAM, CD133, and CD44, at the mRNA and protein levels (PMID:28126340)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Fmr1nb	ENSMUSG00000062170
rattus_norvegicus	Fmr1nb	ENSRNOG00000053397

Protein

Protein identifiers

FMR1 neighbor protein — Q8N0W7 (reviewed: Q8N0W7)

Alternative names: Cancer/testis antigen 37, Sarcoma antigen NY-SAR-35

All UniProt accessions (2): F2Z3J3, Q8N0W7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Tissue specificity. Testis-specific. Expressed in melanoma, sarcoma, lung, breast, bladder, esophageal and ovarian cancers.

RefSeq proteins (1): NP_689791* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR055331	FMR1-like	Family

UniProt features (10 total): topological domain 3, transmembrane region 2, chain 1, domain 1, region of interest 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N0W7-F1	61.95	0.01

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 32 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_UP, WHITEHURST_PACLITAXEL_SENSITIVITY, TERAMOTO_OPN_TARGETS_CLUSTER_1, MCCLUNG_COCAIN_REWARD_4WK, MIKKELSEN_ES_ICP_WITH_H3K4ME3, chrXq27, PASINI_SUZ12_TARGETS_UP, FOSTER_KDM1A_TARGETS_UP, GCNP_SHH_UP_LATE.V1_UP, PKCA_DN.V1_UP, MIR6734_5P, GSE1448_ANTI_VALPHA2_VS_VBETA5_DP_THYMOCYTE_DN, GSE17721_CPG_VS_GARDIQUIMOD_6H_BMDC_UP, DESCARTES_MAIN_FETAL_ANTIGEN_PRESENTING_CELLS, FOURATI_BLOOD_TWINRIX_AGE_25_83YO_RESPONDERS_VS_POOR_RESPONDERS_0DY_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

450 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FMR1NB	NXF2B	Q9GZY0	641
FMR1NB	CXorf51A	A0A1B0GTR3	582
FMR1NB	AFF2	P51816	558
FMR1NB	SLITRK2	Q9H156	550
FMR1NB	HSFX4	A0A1B0GTS1	542
FMR1NB	FAM209B	Q5JX69	511
FMR1NB	CCDC83	Q8IWF9	507
FMR1NB	FATE1	Q969F0	507
FMR1NB	SWT1	Q5T5J6	500
FMR1NB	FMR1	Q06787	491
FMR1NB	SPANXD	Q9BXN6	478
FMR1NB	STARD6	P59095	470
FMR1NB	PAGE4	O60829	464
FMR1NB	MAGEC1	O60732	461
FMR1NB	ACRBP	Q8NEB7	446
FMR1NB	EOLA2	Q96DE9	446

IntAct

5 interactions, top by confidence:

A	B	Type	Score
FMR1NB	WT1	psi-mi:“MI:0915”(physical association)	0.370
FMR1NB	NOP56	psi-mi:“MI:0914”(association)	0.350
FMR1NB	NRDC	psi-mi:“MI:0914”(association)	0.350
FMR1NB	ODR4	psi-mi:“MI:0914”(association)	0.350

BioGRID (25): NOP56 (Affinity Capture-MS), CEBPZ (Affinity Capture-MS), RRP12 (Affinity Capture-MS), RPL26L1 (Affinity Capture-MS), NRD1 (Affinity Capture-MS), CWC22 (Affinity Capture-MS), CHCHD2P9 (Affinity Capture-MS), PITHD1 (Affinity Capture-MS), CWC22 (Affinity Capture-MS), CEBPZ (Affinity Capture-MS), NRD1 (Affinity Capture-MS), RPL26L1 (Affinity Capture-MS), NOP56 (Affinity Capture-MS), BOP1 (Affinity Capture-MS), RRP12 (Affinity Capture-MS)

ESM2 similar proteins: A0A0A6YXX9, A0A1Z2R986, A0A2R8Y4Y8, A0A2R8YFL7, A0A2R8YFM6, A0A8J1K1A4, A6NHS7, A8MZH6, G5E8D7, O00237, O54767, O77726, O88393, P09258, P13374, P20239, P26342, P35054, P47983, P47984, P70041, Q03167, Q05996, Q07G34, Q14CH0, Q2Q0J1, Q499E0, Q4FZG8, Q4V7E2, Q5XJY6, Q69555, Q6P995, Q6UQ28, Q76B58, Q77MP7, Q77NN4, Q800X4, Q86WS3, Q8K1M7, Q8N0W7

Diamond homologs: Q80ZA7, Q8N0W7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

43 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	23
Likely benign	8
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

815 predictions. Top by Δscore:

Variant	Effect	Δscore
X:147981680:G:GA	donor_loss	1.0000
X:147981680:G:GG	donor_gain	1.0000
X:147981681:T:G	donor_loss	1.0000
X:148003195:CTTAA:C	acceptor_loss	1.0000
X:148003196:TTAAG:T	acceptor_loss	1.0000
X:148003198:A:AG	acceptor_gain	1.0000
X:148003198:AAG:A	acceptor_gain	1.0000
X:148003198:AAGG:A	acceptor_gain	1.0000
X:148003199:A:AG	acceptor_gain	1.0000
X:148003199:A:C	acceptor_loss	1.0000
X:148003199:AG:A	acceptor_gain	1.0000
X:148003200:G:A	acceptor_gain	1.0000
X:148003200:G:GG	acceptor_gain	1.0000
X:148003200:G:GT	acceptor_loss	1.0000
X:148003223:A:AG	acceptor_gain	1.0000
X:148003223:AAAT:A	acceptor_gain	1.0000
X:148003223:AAATG:A	acceptor_gain	1.0000
X:148003224:A:G	acceptor_gain	1.0000
X:148003316:AACAA:A	donor_gain	1.0000
X:148003317:ACAA:A	donor_gain	1.0000
X:148003317:ACAAG:A	donor_loss	1.0000
X:148003318:CAA:C	donor_gain	1.0000
X:148003318:CAAG:C	donor_loss	1.0000
X:148003319:AA:A	donor_gain	1.0000
X:148003320:AGTA:A	donor_loss	1.0000
X:148003321:G:GG	donor_gain	1.0000
X:148003321:GT:G	donor_loss	1.0000
X:148006684:A:G	acceptor_gain	1.0000
X:148006690:T:A	acceptor_gain	1.0000
X:148006700:A:G	acceptor_gain	1.0000

AlphaMissense

1685 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:148008659:A:C	S194R	0.974
X:148008661:C:A	S194R	0.974
X:148008661:C:G	S194R	0.974
X:148006791:T:C	F163L	0.953
X:148006793:T:A	F163L	0.953
X:148006793:T:G	F163L	0.953
X:148006824:T:C	F174L	0.948
X:148006826:T:A	F174L	0.948
X:148006826:T:G	F174L	0.948
X:148006770:T:A	C156S	0.924
X:148006771:G:C	C156S	0.924
X:148006821:T:A	C173S	0.916
X:148006822:G:C	C173S	0.916
X:148006821:T:C	C173R	0.910
X:148006737:T:A	C145S	0.901
X:148006738:G:C	C145S	0.901
X:148006704:T:A	C134S	0.899
X:148006705:G:C	C134S	0.899
X:148006770:T:C	C156R	0.888
X:148006788:T:A	C162S	0.885
X:148006789:G:C	C162S	0.885
X:148006785:T:A	C161S	0.884
X:148006786:G:C	C161S	0.884
X:148006737:T:C	C145R	0.868
X:148006792:T:G	F163C	0.867
X:148006738:G:A	C145Y	0.864
X:148006704:T:C	C134R	0.861
X:148006788:T:C	C162R	0.861
X:148006785:T:C	C161R	0.859
X:148006790:T:G	C162W	0.859

dbSNP variants (sampled 300 via entrez): RS1000097576 (X:148005110 G>A), RS1000166641 (X:148003420 G>A,C), RS1000213452 (X:147988336 C>G,T), RS1000270253 (X:147996691 A>G,T), RS1000303134 (X:147980725 A>G), RS1000343446 (X:148013035 T>C), RS1000500211 (X:147990226 C>T), RS1000699674 (X:147990565 G>T), RS1000816367 (X:147988749 T>C), RS1001010457 (X:147998372 C>T), RS1001012537 (X:148022504 A>G), RS1001078520 (X:148021836 G>C), RS1001091419 (X:147982375 C>T), RS1001124403 (X:148006218 A>G), RS1001881962 (X:147997652 A>G,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001613_16	Antineutrophil cytoplasmic antibody-associated vasculitis	2.000000e-08
GCST009391_1046	Metabolite levels	1.000000e-06
GCST009391_1571	Metabolite levels	6.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010516	orotic acid measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases methylation, increases expression	2
aflatoxin B2	increases methylation	1
gallium arsenide	increases expression	1
Decitabine	increases expression	1
Valproic Acid	increases methylation	1
Copper Sulfate	affects expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.